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https://www.readbyqxmd.com/read/28453671/wright-fisher-exact-solver-wfes-scalable-analysis-of-population-genetic-models-without-simulation-or-diffusion-theory
#1
Ivan Krukov, Bianca de Sanctis, A P Jason de Koning
Motivation: The simplifying assumptions that are used widely in theoretical population genetics may not always be appropriate for empirical population genetics. General computational approaches that do not require the assumptions of classical theory are therefore quite desirable. One such general approach is provided by the theory of absorbing Markov chains, which can be used to obtain exact results by directly analyzing population genetic Markov models, such as the classic bi-allelic Wright-Fisher model...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453653/the-bologna-annotation-resource-bar-3-0-improving-protein-functional-annotation
#2
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449343/cost-effectiveness-of-the-highly-effective-direct-acting-antivirals-in-the-treatment-of-chronic-hepatitis-c-in-hong-kong
#3
Angeline Oi-Shan Lo, Henry Lik-Yuen Chan, Vincent Wai-Sun Wong, Grace Lai-Hung Wong
BACKGROUND AND AIM: In Asia-Pacific where cost is a major concern, peginterferon plus ribavirin (PR) often remain as the standard of care in chronic hepatitis C (CHC) treatment, while the direct-acting antivirals (DAAs) are commonly recommended as retreatment. Newer DAAs can achieve a sustained virological response (SVR) of nearly 100% with pan-genotypic coverage, that is "Highly Effective DAAs." We aimed to investigate the most desirable cost range for the Highly Effective DAAs using Hong Kong as an example...
May 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28448739/health-economic-evaluation-of-immunization-strategies-of-hepatitis-e-vaccine-for-elderly-population
#4
Xiaoqing Cheng, Yueyuan Zhao, Xuefeng Zhang, Hui Jin, Jin Min
Objective This study was conducted to assess the cost-effectiveness of hepatitis E vaccination of elderly population in the sporadic regions in China. Methods We used a decision tree-Markov model to evaluate the cost-effectiveness of three kinds of hepatitis E virus vaccination strategies from societal perspectives. Parameter estimates were obtained from published researches and experts' opinion. The time horizon was 16 years, and the discounted rate was 3% annually. Costs are expressed in 2016 US dollars...
April 27, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28448451/time-aware-service-ranking-prediction-in-the-internet-of-things-environment
#5
Yuze Huang, Jiwei Huang, Bo Cheng, Shuqing He, Junliang Chen
With the rapid development of the Internet of things (IoT), building IoT systems with high quality of service (QoS) has become an urgent requirement in both academia and industry. During the procedures of building IoT systems, QoS-aware service selection is an important concern, which requires the ranking of a set of functionally similar services according to their QoS values. In reality, however, it is quite expensive and even impractical to evaluate all geographically-dispersed IoT services at a single client to obtain such a ranking...
April 27, 2017: Sensors
https://www.readbyqxmd.com/read/28447309/markov-decision-process-measurement-model
#6
Michelle M LaMar
Within-task actions can provide additional information on student competencies but are challenging to model. This paper explores the potential of using a cognitive model for decision making, the Markov decision process, to provide a mapping between within-task actions and latent traits of interest. Psychometric properties of the model are explored, and simulation studies report on parameter recovery within the context of a simple strategy game. The model is then applied to empirical data from an educational game...
April 26, 2017: Psychometrika
https://www.readbyqxmd.com/read/28445594/porcine-milk-induces-a-strengthening-of-barrier-function-in-porcine-jejunal-epithelium-in-vitro
#7
Judith Radloff, Silke S Zakrzewski, Robert Pieper, Alexander G Markov, Salah Amasheh
Milk contains a variety of components that have been shown to affect the expression and localization of epithelial tight junction proteins and therefore the intestinal barrier. Thus, we hypothesized that milk would have an effect on intestinal barrier properties, owing to effects on the tight junction in an intraspecies porcine intestinal in vitro model. Jejunal samples of piglets derived from different age groups were analyzed. Transepithelial electrical resistance was recorded employing the Ussing chamber technique...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28445256/cost-effectiveness-analysis-of-ultrasonography-screening-for-nonalcoholic-fatty-liver-disease-in-metabolic-syndrome-patients
#8
Pochamana Phisalprapa, Siripen Supakankunti, Phunchai Charatcharoenwitthaya, Piyaporn Apisarnthanarak, Aphinya Charoensak, Chaiwat Washirasaksiri, Weerachai Srivanichakorn, Nathorn Chaiyakunapruk
BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) can be diagnosed early by noninvasive ultrasonography; however, the cost-effectiveness of ultrasonography screening with intensive weight reduction program in metabolic syndrome patients is not clear. This study aims to estimate economic and clinical outcomes of ultrasonography in Thailand. METHODS: Cost-effectiveness analysis used decision tree and Markov models to estimate lifetime costs and health benefits from societal perspective, based on a cohort of 509 metabolic syndrome patients in Thailand...
April 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28444905/the-value-of-a-combined-word-recognition-and-knowledge-measure-to-understand-characteristics-of-our-patients-oral-health-literacy
#9
Kathryn A Atchison, Mark D Macek, Daniela Markovic
OBJECTIVE: The objective of the analysis was to examine the association between sociodemographic and dental understanding and utilization characteristics and lower oral health literacy (HL) and knowledge. METHODS: The cross-sectional Multicenter Oral Health Literacy Research Study (MOHLRS) recruited and interviewed 923 English-speaking, initial care-seeking adults. The questionnaire included participant sociodemographic characteristics, measures of the participant's understanding and utilization of dentistry, and two oral HL measures, the Rapid Estimate of Adult Literacy in Medicine and Dentistry (REALM-D) and the Comprehensive Measure of Oral Health Knowledge (CMOHK), which were combined into a new composite HL and knowledge measure, the MOHLR-K...
April 26, 2017: Community Dentistry and Oral Epidemiology
https://www.readbyqxmd.com/read/28444187/modelling-the-cost-effectiveness-pcsk9-inhibitors-vs-ezetimibe-through-ldl-c-reductions-in-a-norwegian-setting
#10
Max Korman, Torbjørn Wisløff
Aims: Despite the success of statins, there remains unmet clinical need in cardiovascular disease (CVD) prevention. New proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors reduce low-density lipoprotein cholesterol (LDL-C) by 55-65%. Two PCSK9 inhibitors, evolocumab and alirocumab, were approved for use in Norway but not yet for reimbursement through public national insurance. We aim to explore the cost-effectiveness of these compared to available treatments in a Norwegian setting...
April 21, 2017: European Heart Journal. Cardiovascular Pharmacotherapy
https://www.readbyqxmd.com/read/28443037/analyzing-dyadic-sequence-data-research-questions-and-implied-statistical-models
#11
Peter Fuchs, Fridtjof W Nussbeck, Nathalie Meuwly, Guy Bodenmann
The analysis of observational data is often seen as a key approach to understanding dynamics in romantic relationships but also in dyadic systems in general. Statistical models for the analysis of dyadic observational data are not commonly known or applied. In this contribution, selected approaches to dyadic sequence data will be presented with a focus on models that can be applied when sample sizes are of medium size (N = 100 couples or less). Each of the statistical models is motivated by an underlying potential research question, the most important model results are presented and linked to the research question...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28441487/the-isomeric-preference-of-an-atypical-dopamine-transporter-inhibitor-contributes-to-its-selection-of-the-transporter-conformation
#12
Ara M Abramyan, Sebastian Stolzenberg, Zheng Li, Claus J Loland, Frank Noé, Lei Shi
Cocaine, a widely abused psychostimulant, inhibits the dopamine transporter (DAT) by trapping the protein in an outward-open conformation, whereas atypical DAT inhibitors such as benztropine have low abuse liability and prefer less outward-open conformations. Here, we use a spectrum of computational modeling and simulation approaches to obtain the underlying molecular mechanism in atomistic detail. Interestingly, our quantum mechanical calculations and molecular dynamics (MD) simulations suggest that a benztropine derivative JHW007 prefers a different stereoisomeric conformation of tropane in binding to DAT compared to that of a cocaine derivative, CFT...
April 25, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28441087/using-the-payoff-time-in-decision-analytic-models-a-case-study-for-using-statins-in-primary-prevention
#13
Alexander Thompson, Bruce Guthrie, Katherine Payne
BACKGROUND: The payoff time represents an estimate of when the benefits of an intervention outweigh the costs. It is particularly useful for benefit-harm decision making for interventions that have deferred benefits but upfront harms. The aim of this study was to expand the application of the payoff time and provide an example of its use within a decision-analytic model. METHODS: Three clinically relevant patient vignettes based on varying levels of estimated 10-year cardiovascular risk (10%, 15%, 20%) were developed...
March 1, 2017: Medical Decision Making: An International Journal of the Society for Medical Decision Making
https://www.readbyqxmd.com/read/28437473/molecular-simulations-and-markov-state-modeling-reveal-the-structural-diversity-and-dynamics-of-a-theophylline-binding-rna-aptamer-in-its-unbound-state
#14
Becka M Warfield, Peter C Anderson
RNA aptamers are oligonucleotides that bind with high specificity and affinity to target ligands. In the absence of bound ligand, secondary structures of RNA aptamers are generally stable, but single-stranded and loop regions, including ligand binding sites, lack defined structures and exist as ensembles of conformations. For example, the well-characterized theophylline-binding aptamer forms a highly stable binding site when bound to theophylline, but the binding site is unstable and disordered when theophylline is absent...
2017: PloS One
https://www.readbyqxmd.com/read/28437451/predicting-explorative-motor-learning-using-decision-making-and-motor-noise
#15
Xiuli Chen, Kieran Mohr, Joseph M Galea
A fundamental problem faced by humans is learning to select motor actions based on noisy sensory information and incomplete knowledge of the world. Recently, a number of authors have asked whether this type of motor learning problem might be very similar to a range of higher-level decision-making problems. If so, participant behaviour on a high-level decision-making task could be predictive of their performance during a motor learning task. To investigate this question, we studied performance during an explorative motor learning task and a decision-making task which had a similar underlying structure with the exception that it was not subject to motor (execution) noise...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28436865/video-anomaly-detection-with-compact-feature-sets-for-online-performance
#16
Roberto Leyva, Victor Sanchez, Chang-Tsun Li
Over the past decade, video anomaly detection has been explored with remarkable results. However, research on methodologies suitable for online performance is still very limited. In this paper, we present an online framework for video anomaly detection. The key aspect of our framework is a compact set of highly descriptive features, which is extracted from a novel cell structure that helps to define support regions in a coarse-to-fine fashion. Based on the scene's activity, only a limited number of support regions are processed, thus limiting the size of the feature set...
April 18, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28435964/kinetics-of-co2-diffusion-in-human-carbonic-anhydrase-a-study-using-molecular-dynamics-simulations-and-the-markov-state-model
#17
Gong Chen, Xian Kong, Diannan Lu, Jianzhong Wu, Zheng Liu
Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 shows its preferential accumulation within a hydrophobic domain in the protein core region...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28435123/is-having-similar-eye-movement-patterns-during-face-learning-and-recognition-beneficial-for-recognition-performance-evidence-from-hidden-markov-modeling
#18
Tim Chuk, Antoni B Chan, Janet Hsiao
The hidden Markov model (HMM)-based approach for eye movement analysis is able to reflect individual differences in both spatial and temporal aspects of eye movements. Here we used this approach to understand the relationship between eye movements during face learning and recognition, and its association with recognition performance. We discovered holistic (i.e., mainly looking at the face center) and analytic (i.e., specifically looking at the two eyes in addition to the face center) patterns during both learning and recognition...
April 20, 2017: Vision Research
https://www.readbyqxmd.com/read/28434864/sensorimotor-representations-in-cerebellar-granule-cells-in-larval-zebrafish-are-dense-spatially-organized-and-non-temporally-patterned
#19
Laura D Knogler, Daniil A Markov, Elena I Dragomir, Vilim Štih, Ruben Portugues
A fundamental question in neurobiology is how animals integrate external sensory information from their environment with self-generated motor and sensory signals in order to guide motor behavior and adaptation. The cerebellum is a vertebrate hindbrain region where all of these signals converge and that has been implicated in the acquisition, coordination, and calibration of motor activity. Theories of cerebellar function postulate that granule cells encode a variety of sensorimotor signals in the cerebellar input layer...
April 14, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28434387/cost-utility-of-biological-treatment-sequences-for-luminal-crohn-s-disease-in-europe
#20
Fanni Rencz, László Gulácsi, Márta Péntek, Krisztina B Gecse, Axel Dignass, Jonas Halfvarson, Fernando Gomollón, Petra Baji, Laurent Peyrin-Biroulet, Péter L Lakatos, Valentin Brodszky
OBJECTIVES: To compare the cost-effectiveness of treatment sequences with available biologics, including adalimumab (ADA), biosimilar infliximab (bsIFX), originator infliximab (IFX) and vedolizumab (VEDO) for luminal Crohn's disease in nine European countries. METHODS: A Markov-model was constructed to simulate five-year medical costs and quality-adjusted life years (QALYs). Data on clinical efficacy were obtained from randomised controlled trials. Country-specific unit costs, discount rates and a third-party payer perspective were applied...
April 24, 2017: Expert Review of Pharmacoeconomics & Outcomes Research
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